Structure of PDB 2olo Chain A Binding Site BS01

Receptor Information

>2olo Chain A (length=393) Species: 1932 (Streptomyces tendae)

TESYDVVVVGGGPVGLATAWQVAERGHRVLVLERHTFFNENGGTSGAERH
WRLQYTQEDLFRLTLETLPLWRALESRCERRLIHEIGSLWFGDTDVVTNE
GQISGTAAMMDKLSVRYEWLKATDIERRFGFRGLPRDYEGFLQPDGGTID
VRGTLAALFTLAQAAGATLRAGETVTELVPDADGVSVTTDRGTYRAGKVV
LACGPYTNDLLEPLGARLAYSVYEMAIAAYRQATPVTEAPFWFAFQQPTP
QDTNLFYGFGHNPWAPGEFVRCGPDFEVDPLDHPSAATGVADRRQMDRLS
GWLRDHLPTVDPDPVRTSTCLAVLPTDPERQFFLGTARDLMTHGEKLVVY
GAGWAFKFVPLFGRICADLAVEDSTAYDISRLAPQSALLEHHH

Ligand information

• Ligand ID: FAD
• InChI: InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
• InChIKey: VWWQXMAJTJZDQX-UYBVJOGSSA-N
• SMILES:
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
  ACDLabs 10.04: O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
• Formula: C27 H33 N9 O15 P2
• Name: FLAVIN-ADENINE DINUCLEOTIDE
• ChEMBL: CHEMBL1232653
• DrugBank: DB03147
• ZINC: ZINC000008215434
• PDB chain: 2olo Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2olo NikD, an unusual amino acid oxidase essential for nikkomycin biosynthesis: structures of closed and open forms at 1.15 and 1.90 A resolution
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): G11 G13 P14 V15 L33 E34 R35 G43 G44 T45 R50 H51 V176 C204 G205 Y207 C321 L322 Y351 W355 A356 F357 K358
• Binding residue (residue number reindexed from 1): G10 G12 P13 V14 L32 E33 R34 G42 G43 T44 R49 H50 V175 C203 G204 Y206 C320 L321 Y350 W354 A355 F356 K357
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): S46 E49 R50 R53 E101 Y258 R272 D276 R305 C321 W355 K358
• Catalytic site (residue number reindexed from 1): S45 E48 R49 R52 E100 Y257 R271 D275 R304 C320 W354 K357

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0008115 sarcosine oxidase activity
• GO:0016491 oxidoreductase activity
• GO:0050660 flavin adenine dinucleotide binding

External links

• PDB: RCSB:2olo, PDBe:2olo, PDBj:2olo
• PDBsum: 2olo
• PubMed: 17697998
• UniProt: Q9X9P9